This one is not my doing, it’s not really a bug either 
The reactor has “exploded” or rather is constantly exploding each tick (because the heat in the reactor never decreases below explosion territory) and removing the rods (but not updating the model), but Greg disabled the actual explosion that would remove the reactor block (and surrounding area) entirely “until Reactor System has been tested well enough” (MultiTileEntityReactorCore2x2.java, line 204).
The easy fix is to re-enable the explosion of the two reactor blocks.